Variant report

Variant	rs12891258
Chromosome Location	chr14:39608892-39608893
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:39606418..39609970-chr14:39637610..39641065,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182400	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10130972	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10133797	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10136536	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10149120	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10151683	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12147991	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12437405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12894046	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12895751	0.83[EUR][1000 genomes]
rs13379360	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17108846	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2737721	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2737729	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2753606	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28379470	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28485301	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2869	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28856917	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34816815	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35035794	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3759545	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4143954	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4902405	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4902406	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4902418	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4902431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4902435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4902448	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs532	0.80[EUR][1000 genomes]
rs57653321	0.84[AFR][1000 genomes]
rs58851254	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67248626	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71407780	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7147194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7153124	0.81[AMR][1000 genomes]
rs73291544	0.84[AFR][1000 genomes]
rs8006879	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9322994	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3429206	chr14:39160730-39648836	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1051247	chr14:39604035-39652789	Genic enhancers Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12891258	TRAPPC6B	cis	multi-tissue	Pritchard
rs12891258	SIP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39583800-39626000	Weak transcription	Spleen	Spleen
2	chr14:39584000-39615000	Weak transcription	Pancreas	Pancrea
3	chr14:39584000-39623600	Weak transcription	Esophagus	oesophagus
4	chr14:39584200-39610800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr14:39584200-39636000	Weak transcription	Small Intestine	intestine
6	chr14:39584200-39638600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr14:39584400-39617200	Weak transcription	Psoas Muscle	Psoas
8	chr14:39584400-39620800	Weak transcription	Colonic Mucosa	Colon
9	chr14:39584400-39626600	Weak transcription	Aorta	Aorta
10	chr14:39584600-39609600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr14:39584600-39625800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr14:39586600-39610600	Strong transcription	HepG2	liver
13	chr14:39587200-39609600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr14:39588600-39635400	Weak transcription	Fetal Brain Male	brain
15	chr14:39589200-39609200	Weak transcription	Gastric	stomach
16	chr14:39589200-39610000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr14:39589200-39618000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr14:39589200-39626400	Weak transcription	Fetal Heart	heart
19	chr14:39592600-39622200	Weak transcription	Right Ventricle	heart
20	chr14:39592800-39618000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr14:39592800-39626600	Weak transcription	NHLF	lung
22	chr14:39594000-39620800	Weak transcription	Hela-S3	cervix
23	chr14:39596200-39621200	Weak transcription	Brain Substantia Nigra	brain
24	chr14:39597800-39610000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr14:39598000-39612600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr14:39598600-39609200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr14:39598600-39610600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr14:39598600-39618000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr14:39598800-39609600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr14:39598800-39636200	Weak transcription	Stomach Mucosa	stomach
31	chr14:39600000-39609600	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr14:39601000-39611400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr14:39601200-39610600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr14:39602200-39609600	Weak transcription	Thymus	Thymus
35	chr14:39602400-39610000	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr14:39602800-39610000	Strong transcription	Adipose Nuclei	Adipose
37	chr14:39602800-39610400	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr14:39603000-39611600	Strong transcription	Fetal Muscle Trunk	muscle
39	chr14:39603600-39609600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr14:39603600-39617200	Weak transcription	Left Ventricle	heart
41	chr14:39604200-39610200	Strong transcription	Fetal Intestine Large	intestine
42	chr14:39604200-39610600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr14:39604200-39617000	Weak transcription	NHDF-Ad	bronchial
44	chr14:39604400-39610800	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr14:39604400-39635400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr14:39604800-39622400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr14:39605000-39611000	Weak transcription	Placenta	Placenta
48	chr14:39605200-39621200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr14:39605400-39609000	Strong transcription	NH-A	brain
50	chr14:39605800-39625200	Weak transcription	HSMMtube	muscle

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